I am having this issue atm. (2.6.3). I originally thought it might have been because of the F3 dog Armour mod I am using that I converted with the TTW script. Looks like you guys are on it. Nice.

I'll try the console resurrect command to see if that works, but I suspect it's only a temporary fix, similar to equipping/unequipping Dogmeat's armour/pack. It reverts back to levitating eyes come the first battle.

And yes, the Nivea fix as well as the other earlier one does not work for this problem.